Quality Filters

The Quality Filters in Emedgene allow you to refine variant review by applying quality-based thresholds. This ensures only variants meeting specific confidence metrics are prioritized for interpretation. Filters can be applied in Simple or Advanced modes and include additional filtering by Calling Methodology for improved CNV and variant type assessment.

Modes

1. Simple Mode

• Quickly filter variants by overall sequencing quality: Low, Moderate, or High.

• Ideal for quick reviews where detailed parameter control is not required.

2. Advanced Mode

Provides fine-grained control over multiple quality metrics depending on the variant type.

Quality Filter

• Options: Low, Moderate, High

• Determines overall confidence score thresholds for all variant types.

VCF Filter

• Options: Pass, Other values

• Filters variants based on their VCF status flag from upstream analysis.

Calling Methodology filter

A. SNVs, Indels, and STRs

• Mapping Quality (MQ): Minimum MQ (0–60); higher values increase confidence.

• Depth (DP): Minimum read depth (0–500; customizable via text box).

• Alternate Read Count: Minimum number of reads supporting the alternate allele (0–500).

• Allele Bias: Filter range 0–100; for mtDNA, represents heteroplasmy levels.

B. SVs, CNVs, and LOH/ROH

• Length: Threshold range (50bp – 100Mb; or Max).

• Bin Count: Minimum number of bins (1–500).

• Likelihood Ratio Score (LRS, DRAGEN 4.3+): Confidence measure for exome/panel CNVs.

• LOH/ROH Regions: Filters variants based on Loss or Runs of Homozygosity status.

Calling methodology filter also allows filtering by variant caller type:

• Small Variant Caller

• CNV Read-Depth Caller

• Forced Genotyping

• Star Allele Caller

• STR Repeat Expansion Caller

• SV Split-End Caller

• Targeted Caller

• MRJD caller

• Array

• Unknown

Note: This is especially useful for filtering CNVs from different callers (e.g., DRAGEN Read-Depth vs. SV Caller) to apply separate noise databases or QC settings.

Default values

When Filters are Reset to Default, The Quality Filters are set to:

• Quality: Moderate and High,

• Mapping Quality ≥45,

• Depth ≥ 10,

• Alternate Read - no filtering,

• Allele bias - no filtering,

• CNV Length - no filtering,

• CNV Bin Count - no filtering.

Tips:

• Start with Simple Mode for quick triaging, then refine using Advanced Mode.

• Apply Calling Methodology filter when reviewing CNVs to avoid cross-caller noise.

• Always cross-check low-quality calls in IGV visualization before discarding.

Warnings

• Quality filtering directly impacts which variants remain for interpretation and reporting.

• Mosaic and high-sensitivity preset filters may require Illumina support.